


Disassembled

by DarkJediQueen



Series: Winter Soldier Cycle [2]
Category: Marvel Cinematic Universe
Genre: M/M
Language: English
Status: Completed
Published: 2014-06-02
Updated: 2014-06-02
Packaged: 2018-02-03 03:43:34
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 4,166
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1729877
Author URL: https://archiveofourown.org/users/DarkJediQueen/pseuds/DarkJediQueen
Summary: <blockquote class="userstuff">
              <p>Now living in Malibu, Tony Stark is getting on with his life as a former Avenger and new head of R&D at Stark Industries. He doesn't dwell on his former life; instead he pushes forward with a new idea along with a new recruit to R&D Maya Hansen.</p>
            </blockquote>





	Disassembled

**Author's Note:**

> I seem to have lost my beta for this story. I wanted to wait to post but I figure I can always edit it later. If any of you wish to volunteer, just let me know in the comments.
> 
> Warnings: This series gets worse before it gets better but please, I almost always do happy endings and this one will have a happy ending.

"Tony, it's a good thing that you put into your contract with SHIELD that all contracts with SHIELD were null and void if you were removed from the Avengers, for any reason. I don't think that they could have used anything you had given them in your current state. Not safely at least." Pepper’s voice was calm and serene even though Tony knew that she was really anything but that. 

"Yeah." Tony leaned back into Pepper, his head on her stomach. Pepper started to card her hands through his hair. She knew that he had been in the workshop for over three days but she knew when to pick her battles. JARVIS had brought up all the footage he had saved from Tony's time the past month or so in the Avengers Tower in New York. At the end of it, she hated Steve so much. There was something else there but she wasn’t sure what it was. There were too many variables and she didn’t have all of them.

Pepper Potts was not a stupid woman. She knew going into the relationship with Tony that he loved someone else that he could never have. She hadn't known at the time that it was Steve Rogers but she knew about the person in general. She knew the second that Tony got a call from Fury about Captain America, the way his face lit up and his body language changed, that this was the person Tony loved. It had been a shock but Tony was like the sun. Anyone would burn themselves to get a feel of it. 

Hearing Bruce's recounting of the first meeting between Tony and Steve, Pepper called him a dick to herself. Hearing the way that Steve talked to him for a long time after that, she still considered him a dick. Tony though fell more in love with him, he saw something in the man that no one else saw. When she broke things off with Tony, Steve had been the one to pick up the pieces and help Tony get sober. Tony, after that, had been good, and he got even better when he called and told her that Steve had agreed to a date. Three weeks of Tony at his best and then dropping to near his worst. The only saving grace had been that he'd stayed sober.

Then a broken Tony and a sad Bruce showed up at the mansion in Malibu, Pepper had brought them in and cared for Tony as best she could. Tony didn't stray from his workshop and Bruce didn't stray too far from him. Pepper still found it funny that the Hulk liked Tony and was worried about him. 

Tony hadn't told her how he had gotten his broken arm and she hadn't pried, instead she just asked JARVIS. The AI took no compunction to hide anything from her. After watching what amounted to ten hours of footage, Pepper contacted Rhodey and sent him the highlights. Three hours and a million dollars later, Rhodey was no longer part of the Air Force and the War Machine outfit was back where it belonged, with Rhodey living in the mansion. Pepper hadn’t figured out why Rhodey wanted that outcome but she did what he wanted. There was something there as well. 

The wagons were circling and she wasn’t sure what SHIELD was going to be in the aftermath.

Two days after that, Pepper had contracts set up with the United States government on contacting Iron Man, Hulk, or War Machine for duty to the United States. She was sure that Fury was still steaming over the costs and regulations on what the three of them could do. The meeting that took place that day with SHIELD, the Avengers, and the lawyers, along with Bruce, Rhodey, and Tony was a meeting to remember. Tony had been vicious and she was sure that SHIELD lawyers still wanted to smoke a cigarette when thinking of the way that she had gone after everything that was Stark Tech that was in their hands. Including their new repulsor engines in their Intercept Helicarriers, whatever that was. Protests had been made but everything had stood that the Stark tech went back where it belonged. SHIELD would have to find a new way to get their helicarriers in the air. 

Tony hadn't looked at the Avengers at all through the meeting, hadn't even said a word to any of them. After Tony had left the room with Bruce, Pepper made Rhodey stay.

"I also want to tell you, Fury, that if any word of any of this gets leaked to any press at any time other than the press statement that SHIELD and SI agreed upon, I will be filing with the federal courts a lawsuit against SHIELD on corporate espionage."

"Corporate espionage?" Steve had asked. Pepper turned to him so quick that Steve could have sworn she should have gotten whiplash. Pepper hadn’t even looked his way the whole time. Now to have her full gaze on him, Steve felt the urge to just apologize but he wasn’t sure what for.

"Natalie Rushman was employed by Stark Industries for many months. SHIELD has the rights to many copyrights as far as technology goes. Natalie Rushman's real name, at least as far as I know, is Natalia Alianovna Romanoff but she goes by Natasha Romanoff. She was around many projects of ours and could have taken what she wanted." 

"That would never fly." Clint practically snorted. 

"Actually it would," Natasha said. She kept her eyes down the entire time. Clint looked at her before looking at Fury. "Stark didn't say a word at the time but he knows that I stole plans."

The lawyers sputtered at her answer but Fury didn't care. He looked Pepper in the eye and nodded. Pepper gathered her things and was almost to the door, with Rhodey behind her when she stopped. "I have some of the techs from SI getting ready to head into the Tower at this time. Anything that is not commercially available to buy on the market is going to be stripped from the Tower except for Jeeves. Tony wants the Tower safe and that means Jeeves stays but remember this, he answers to Tony and I." Pepper looked at Steve as she spoke.

Pepper had loved that day and was very happy that JARVIS had recorded the entire thing for posterity. 

xXxXxXx

"Rhodey and Bruce want to head out on the boat to do some fishing today, I was thinking of some sunbathing. Want to join us?"

Tony smiled up at her and knew from her tone of voice that it wasn't a request. It was masked as a request to give him the illusion that he could back out but he knew that she would make him.

"JARVIS lock down the workshop. I am taking a day for myself."

"I will, Sir. Have fun."

Tony quickly stood up, never quite moving far enough away from Pepper to stop touching her. Pepper knew that he didn't mean anything by what he was doing. He needed comfort and it was as much as he was going to get from her and he knew it, so he took it. 

xXxXxXx

"Are you sure about this project, Tony?" Pepper asked as she sat down in the chair. Tony was beside her looking out the window. He had taken to being the head of R&D really well and the production of the projects that he touched were moving along so fast that Pepper was afraid of running out if Tony stayed in one area too long.

"Maya Hansen's Extremis has many applications. The first of which is one that SHIELD and the government would pay dearly for. It's a nanotech version of the Super Soldier Serum. It's the magic bullet that would give them the army they never got to make in World War II."

Pepper stared at him shocked. "Can it really do that?"

"She says it can, and from what I have read of it...yes. There are other applications of it but that is what it boils down to. This would make Stark Industries the hottest commodity in the medical field. Fast healing, hell Pep, fast everything. Tailor designed to the needs of the person getting it."

"What about misuse?"

Tony looked at her shocked. He knew what she meant but it still stung. "I would have it tested to the best of my ability. There would be constant upgrades to the tech as new batches are made but Pepper...This could cure so much out there in the world."

"Go have your fun. I want constant updates, Tony. I mean it. Don't make me have JARVIS stalk you."

**One Month Later**  
Pepper was standing in her office, with her back to the door looking out upon the city. She hadn't slept in three days and finally several hours before, she admitted that she needed the help of SHIELD. She heard the office door open but didn't turn around.

"Miss Potts, the Avengers are here." Her secretary talked softly. Everyone was treating her with kid gloves but she didn't mind. It meant they also left her alone.

"Send them. Please alert Rhodes that they are here."

"He is with them now."

"Thank you."

When she heard the sound of six shuffling feet, Pepper turned. Natasha, Clint, and Thor were standing right behind the desk while Rhodey was between them and her. Steve and Bucky were at the back of the room. Rhodey was pissed. So was she.

"Thank you for coming as quick as you did."

"Fury told us that we were needed but he did not say why," Steve said as he moved closer to the desk. 

"That's because I would not say why, except to tell him that it was a matter of SHIELD security. Three days ago, while driving around the city, Tony was abducted. Rhodes and Bruce have been looking for him nonstop but have hit a block on all roads. His car was found three blocks from here with no damage to it. There were no cameras that recorded the abduction and since it was around three in the morning, there were no witnesses either."

"He's gone?" Bucky asked. Pepper could hear a small amount of joy in his voice. She didn’t like it. Bucky gave her the creeps. She knew why Tony didn’t like him. There was something about him that was just off. 

"Yes. There has been no ransom demand or anything from the person or persons that took him. There were no prints and no clues left at the scene."

"No idea at all on who would benefit from him being dead?" Natasha asked. 

Pepper turned her cool gaze to the assassin before looking over at Bucky and not answering. Steve's face darkened and he cleared his throat.

"I don't want to start this."

"I did not ask for him,” Pepper nodded at Bucky. “Nor you. I asked for Black Widow and Hawkeye only. I did not ask Fury for the entire Avengers team. I am sorry Thor I mean no disrespect but I don't want to announce to the world that he is missing. All five of your here is too much."

"Fury wants him found, Ma'am and he wants him found now. Stark has too much in his head that could cripple SHIELD if it was found out." Bucky looked pissed as he talked. 

"I understand that but I also want him back alive. I don't want Mr. Barnes anywhere near him." Pepper turned her eyes back to Bucky. "I know the truth of that incident, Barnes. I have the footage. Leave now."

"Miss Potts, Mr. Barnes is a member of the Avengers."

"And I did not call for the Avengers. You have two choices, Captain Rogers. You can take your new boy toy and leave the premises or I can have you thrown in jail for trespassing. I am sure that Fury will get you quickly but not before a reporter snaps a picture. We can't have Captain America getting thrown in jail can we?" Pepper leveled her best gaze that made Tony run and hide at Steve's face. Steve held her gaze for several seconds before he looked away. Without a word he turned, grabbed Bucky's arm, and left the room. "Thor, I have thought of a way that you could help but it would involve you changing into normal clothes."

xXxXxXx

"Why don't you trust him?" Natasha asked Pepper later that night while everyone else was eating. "What incident were you talking about?"

Pepper turned to look at Natasha. She sighed and leaned back in her chair in the living room area. The others were across the room talking tactics and what to do to find Tony.

"What happened to Tony to have Barnes break his arm?" Pepper asked.

"Steve told us that the two were sparring and Stark was running his mouth about...things to Bucky."

"And you never asked to see the footage?"

"Why would Steve or Bucky lie?"

"It was the reason that Tony left. Wouldn't you like to know what caused such a rift?"

"Stark hadn't been in the best mood for weeks. I...Bucky said it was because Tony didn't accept their relationship. I never took Stark to be so jealous. They had only had a few dates, Steve said."

 

Pepper snorted interrupting Natasha.

"The relationship was going well from what I had heard from Tony. Then the call came through and for Steve, Tony no longer existed. Even the rest of you didn't even stop in and say 'Hey, Steve's bringing Bucky home today. Don't you want to meet him?' Instead Steve brings Bucky to Tony's workshop and jumps on him for not being happy that the love of Steve's life is back from the dead and Tony should be so happy at losing someone he cared for."

Natasha ducked her head. Pepper didn't stop though.

"Then Bucky breaks Tony's arm and everyone sides with Steve and Tony is thrown from the Avengers. If you want to see the footage, JARVIS can cue it up. In fact, JARVIS bring it up but don't play it. I want everyone to see it." Pepper stood up and moved over to where the boys were eating and talking. She cleared her throat and Clint and Thor looked at her. Bruce and Rhodey just kept their heads down. JARVIS lowered a screen and started up the footage from the sparring incident. Once Tony was out of his armor, JARVIS brought up the fight between Steve and Tony that night when Steve had gotten home. Clint sucked in a breath when his little confrontation with Tony came up. Then there was the last time that Tony and Steve talked, when Steve told him he was off the Avengers.

"If that is how all of you treat your teammates, I don't want to see how you treat your enemies." Pepper stalked out of the room, heading up to her wing of the house. Bruce and Rhodey followed behind her, taking her dinner and theirs so they could eat together. 

Back in the living room, Thor, Clint, and Natasha didn't say a word nor did they eat. The silence dragged out for the entire night. None of them felt welcome in what had become Tony's protection from them. Instead Clint and Natasha slept on one couch together while Thor slept on the other. 

xXxXxXx

The first breakthrough that came was two days after the Avengers arrived in Malibu. There was a warehouse on the edge of town that had received a supply of medical equipment along with computer tech and was using much more power than it should have. 

That was also the same time that Maya Hansen was brought to Pepper's attention due to the fact she hadn't been in for the past two days. Natasha and Clint were sent to the warehouse while Pepper and Thor checked out Maya's house which was empty of everything. She had skipped town. 

Pepper alerted Clint and Natasha what they could be facing and then went to pick up Rhodey and headed to the warehouse.

The first thing that Pepper saw upon arriving at the warehouse was the man who was trying to kill Rhodey. Rhodey had only arrived minutes before them and he already looked worse than he had after Vanko. His helmet was missing as well as most of his weapons. 

"Situation?" Pepper called over the radio.

"The man that War Machine is fighting was released by Hansen just seconds after War Machine arrived. I have no eyes on Stark but there is a second looking ready to come out of the...cocoon?" Natasha called over the radio. 

"Pepper, I read something heading our way in the air."

"Just get away Rhodey. Thor!" Pepper called and Thor entered into the fray with the other two men. The second that Thor got the man’s attention, Rhodey pulled himself out. He braced himself to fight whatever was coming their way. He kept his eyes on the sky and nearly cried when he saw that it was the carrier of Tony's armor. The carrier went straight through the wall and into the warehouse. Under a minute later, Iron Man burst out. Rhodey had never seen that version of the armor before and wondered which version of the armor Tony was up to. 

"I've got this, Point Break!" Tony yelled before he blasted himself right at the enemy. The fight was over in minutes, with the enemy dead on the ground. Tony’s armor was barely damaged. 

Pepper was the first to approach him.

"Tony?"

Tony popped the faceplate up and it retracted back so that his whole head was visible. He looked no worse for the wear.

"Miss me?" Tony asked. Pepper started to cry and ran forward to him. Tony pulled her into a hug. "Where's Bruce?"

"We didn't know the situation and he stayed back. If Thor hadn't been able to push the man back, then he would have stepped in."

"What about the rest of the Avengers. I know the assassins are here but we are missing Stick Up His Ass and the one who likes to put it there."

"Tony..." Pepper chastised but smiled. "I sent them packing back to New York. I wasn't going to have either of them around you."

"You protect me so well."

"Tony..."

"It was Maya. When she found out that the Avengers were in town, she destroyed Extremis after creating Mallen here. She was going to kill me as well but I was able to hide."

"The cocoon is gone," Clint called over the radio. 

"I destroyed it. Extremis Project is mothballed. Why don't we all head back to the mansion and we can debrief there?" 

xXxXxXx

"I told Hansen the other day that the Project was going to be mothballed. The first set of test DNA used for it, died. Further testing showed that only two point five percent of the population worldwide would be able to have Extremis in them. I was not one of them and that was how she was going to kill me. I stopped her. I had just hacked her systems and called for JARVIS to send me my armor when Clint and Natasha arrived. That distracted her enough that she had to release Mallen to protect her. She wasn't counting on me at all. I wiped the drives she was using and she destroyed the rest. She didn't expect to not have her research. She had a gun pointed at me when my armor burst into the room. When I was fully outfitted, she had turned the gun on herself."

"Who's doing clean up?" Rhodey asked as he placed an ice pack on the back of his head. Tony was on the couch looking fine. In fact, other than few scratches on Thor, everyone was unscathed except for Rhodey, who looked like we went seven rounds with a giant robot with no protection. 

"The military. I had JARVIS call them as soon as I could access him and he had the armor on its way to me. I will give SHIELD my files as soon as I pull all other information out of them. Extremis is not to be used for anything ever."

"Agreed." Natasha and Clint spoke at the same time. 

Tony spent an hour talking with all of them before he went down to his workshop to check up on his robots. Dum-E was the first to greet him and Tony patted him on the head. Butterfingers and Yu were hanging back. Pepper watched from outside the room as Tony talked to his robots. Sometimes she thought that even though he had Rhodey and herself and now Bruce, robots were the only friends he would ever have that didn't disappoint him and they were never disappointed by him. That broke her heart.

xXxXxXx

It was that evening when Tony was fixing himself some food that Pepper noticed he moved better than he ever had. While he acted young, Pepper knew that he had a few aches and pains. The others were all asleep in rooms waiting to go back to New York in the morning. 

Tony was cutting up an apple when he cut his finger. Pepper watched him jerk and stick the finger in his mouth. Pepper moved forward grabbing a towel and pulling the digit out of his mouth. She went to wrap the finger to apply pressure but when she looked she noticed that the finger was now mostly healed. Pepper wiped the remainder of the blood off and she stared.

"Shush," Tony said. Tony grabbed Pepper and pulled her close kissing her. It wasn't until she heard a set of soft footsteps that Pepper started to kiss him back. Whoever they were cleared their throat and Pepper knew it was Natasha. Tony pulled back, giving Natasha a look of disdain for interrupting them.

"Fury called. He wants us home now. Thanks for letting us stay. Clint and Thor are already in the car. I just wanted to say goodbye."

"Thanks for coming to my rescue, Agent," Tony said pulling Pepper back close to his body when she started to pull away. Natasha nodded and Tony gave her until she got out the door before he let Pepper go. "I didn't think she would tell me goodbye."

"Tony, what is going on?"

"I only want to do this once Pep so let’s go to Rhodey and Bruce. Both are in Bruce's lab."

"How do you...Tony!"

"She thought she was killing me. I hacked the records and changed what version of Extremis she gave me. I am not Mallen, Pep."

"What did it do to you?"

"I am still me. I just have some upgrades."

xXxXxXx

After all of them woke up in the late afternoon, Tony decided to treat them all to a nice big dinner. 

"JARVIS, protect my house!" Tony called as he shut the door behind him. 

JARVIS watched as his charges left the house before he brought up a screen in Tony's workshop. He queued up the older footage of Bucky's room in the Tower. Whenever the house was empty, JARVIS queued up the room to watch. He could do it without having it on a screen but having it up, made it all feel more real. 

JARVIS had started a search of all known databases for a match for Bucky's face in their systems over a week ago. JARVIS didn't trust Bucky as far as he could throw him without the use of a robot and since he was an AI, that wasn't any distance at all.

It was an hour later that the database found a hit. Winter Soldier. JARVIS started to hack through the files that SHIELD had on Winter Soldier and found that they knew of him but knew nothing concrete on him.

When Tony and the rest returned home that evening, JARVIS had a printed out file waiting on the coffee table for all four of them. 

Bruce was the first to see them but Tony was the first to look at the files. 

"Is this all?"

"All that I could access, Sir. Your new touch is needed for much more of the files."

"I don't want this going anywhere. I want to present an airtight file to SHIELD. Does it make me a bad person that I want to shove this in all their faces?" 

Bruce laughed a small, derisive laugh while Pepper and Rhodey smiled at him.

Before anyone could say anything, a chirp from Tony's phone alerted him to the fact that someone was calling him. He looked at the number frowning but he answered. 

"How can I help you, Agent Romanoff?"

"Stark, Rogers and Barnes never made it home. We received a letter from HYDRA. They have them."  
 **The End**

**Author's Note:**

> This was almost called "In Which SHIELD and the Avengers find out that Pepper is a BAMF when it comes to protecting Tony" in fact I still call it that in my head.


End file.
